Fix formatting in yaml files, add yamllint config (#1279)

* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

.github/workflows/code-linting.yml

@@ -12,9 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
-        with:
-          node-version: "10"
 
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
@@ -27,9 +25,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
-        with:
-          node-version: "10"
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -44,9 +40,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install NodeJS
-        uses: actions/setup-node@v1
+        uses: actions/setup-node@v2
-        with:
-          node-version: "10"
 
       - name: Install yaml-lint
         run: npm install -g yaml-lint

.yamllint.yml

@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable

modules/abacas/meta.yml

@@ -14,7 +14,7 @@ tools:
       documentation: http://abacas.sourceforge.net/documentation.html
       tool_dev_url: None
       doi: "10.1093/bioinformatics/btp347"
-      licence: ['GPL v2-or-later']
+      licence: ["GPL v2-or-later"]
 
 input:
   - meta:

modules/adapterremoval/meta.yml

@@ -10,7 +10,7 @@ tools:
       description: The AdapterRemoval v2 tool for merging and clipping reads.
       homepage: https://github.com/MikkelSchubert/adapterremoval
       documentation: https://adapterremoval.readthedocs.io
-        licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/agrvate/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://github.com/VishnuRaghuram94/AgrVATE
       tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/amps/meta.yml

@@ -24,7 +24,7 @@ tools:
       documentation: "https://github.com/keyfm/amps"
       tool_dev_url: "https://github.com/keyfm/amps"
       doi: "10.1186/s13059-019-1903-0"
-      licence: ['GPL >=3']
+      licence: ["GPL >=3"]
 
 input:
   - maltextract_results:

modules/arriba/meta.yml

@@ -10,7 +10,7 @@ tools:
       documentation: https://arriba.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/suhrig/arriba
       doi: "10.1101/gr.257246.119"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/artic/guppyplex/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://artic.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/artic-network/fieldbioinformatics
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/artic/minion/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://artic.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/artic-network/fieldbioinformatics
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/assemblyscan/meta.yml

@@ -10,7 +10,7 @@ tools:
       documentation: https://github.com/rpetit3/assembly-scan
       tool_dev_url: https://github.com/rpetit3/assembly-scan
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/ataqv/ataqv/meta.yml

@@ -9,7 +9,7 @@ tools:
       documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
       tool_dev_url: https://github.com/ParkerLab/ataqv
       doi: "https://doi.org/10.1016/j.cels.2020.02.009"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/bakta/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://github.com/oschwengers/bakta
       tool_dev_url: https://github.com/oschwengers/bakta
       doi: "10.1099/mgen.0.000685"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/bamaligncleaner/meta.yml

@@ -8,7 +8,7 @@ tools:
       homepage: https://github.com/maxibor/bamAlignCleaner
       documentation: https://github.com/maxibor/bamAlignCleaner
       tool_dev_url: https://github.com/maxibor/bamAlignCleaner
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/bamcmp/meta.yml

@@ -10,14 +10,15 @@ keywords:
 
 tools:
   - bamcmp:
-      description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
+      description:
+        Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
         sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
         reads which multimap to the contamination genome will be spuriously kept.
       homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
       documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
       tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
       doi: "10.1158/1541-7786.MCR-16-0431"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/bamtools/convert/meta.yml

@@ -19,7 +19,7 @@ tools:
       documentation: https://github.com/pezmaster31/bamtools/wiki
       tool_dev_url: http://github.com/pezmaster31/bamtools
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/bamtools/split/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/pezmaster31/bamtools/wiki
       tool_dev_url: http://github.com/pezmaster31/bamtools
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/bamutil/trimbam/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
       tool_dev_url: https://github.com/statgen/bamUtil
       doi: "10.1101/gr.176552.114"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/bandage/image/meta.yml

@@ -11,7 +11,7 @@ tools:
       Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
     homepage: https://github.com/rrwick/Bandage
     documentation: https://github.com/rrwick/Bandage
-        licence: ['GPL-3.0-or-later']
+    licence: ["GPL-3.0-or-later"]
 input:
   - meta:
     type: map

modules/bbmap/align/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
       tool_dev_url: None
       doi: ""
-      licence: ['UC-LBL license (see package)']
+      licence: ["UC-LBL license (see package)"]
 
 input:
   - meta:

modules/bbmap/bbduk/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
       tool_dev_url: None
       doi: ""
-      licence: ['UC-LBL license (see package)']
+      licence: ["UC-LBL license (see package)"]
 
 input:
   - meta:

modules/bbmap/bbsplit/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
       tool_dev_url: None
       doi: ""
-      licence: ['UC-LBL license (see package)']
+      licence: ["UC-LBL license (see package)"]
 
 input:
   - meta:

modules/bbmap/index/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
       tool_dev_url: None
       doi: ""
-      licence: ['UC-LBL license (see package)']
+      licence: ["UC-LBL license (see package)"]
 
 input:
   - fasta:

modules/bcftools/concat/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/consensus/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/filter/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/index/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: https://samtools.github.io/bcftools/howtos/index.html
       tool_dev_url: https://github.com/samtools/bcftools
       doi: "10.1093/gigascience/giab008"
-      licence: ['MIT', 'GPL-3.0-or-later']
+      licence: ["MIT", "GPL-3.0-or-later"]
 
 input:
   - meta:

modules/bcftools/isec/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/merge/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/mpileup/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/norm/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/query/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/reheader/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
       doi: 10.1093/gigascience/giab008
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/bcftools/sort/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: http://www.htslib.org/doc/bcftools.html
       tool_dev_url: https://github.com/samtools/bcftools
       doi: "10.1093/bioinformatics/btp352"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/bcftools/stats/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bcftools/view/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://samtools.github.io/bcftools/bcftools.html
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/bamtobed/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/complement/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/genomecov/meta.yml

@@ -9,7 +9,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/getfasta/meta.yml

@@ -9,7 +9,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - bed:
       type: file

modules/bedtools/intersect/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/makewindows/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
       tool_dev_url: None
       doi: "10.1093/bioinformatics/btq033"
-      licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/maskfasta/meta.yml

@@ -9,7 +9,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/merge/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/slop/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/sort/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bedtools/subtract/meta.yml

@@ -10,7 +10,7 @@ tools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
-        licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/biobambam/bammarkduplicates2/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: https://gitlab.com/german.tischler/biobambam2
       documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
       doi: 10.1186/1751-0473-9-13
-        licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

modules/bismark/align/meta.yml

@@ -17,7 +17,7 @@ tools:
       homepage: https://github.com/FelixKrueger/Bismark
       documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
       doi: 10.1093/bioinformatics/btr167
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/bismark/deduplicate/meta.yml

@@ -19,7 +19,7 @@ tools:
       homepage: https://github.com/FelixKrueger/Bismark
       documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
       doi: 10.1093/bioinformatics/btr167
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/bismark/genomepreparation/meta.yml

@@ -19,7 +19,7 @@ tools:
       homepage: https://github.com/FelixKrueger/Bismark
       documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
       doi: 10.1093/bioinformatics/btr167
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - fasta:
       type: file

modules/bismark/methylationextractor/meta.yml

@@ -18,7 +18,7 @@ tools:
       homepage: https://github.com/FelixKrueger/Bismark
       documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
       doi: 10.1093/bioinformatics/btr167
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/bismark/report/meta.yml

@@ -16,7 +16,7 @@ tools:
       homepage: https://github.com/FelixKrueger/Bismark
       documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
       doi: 10.1093/bioinformatics/btr167
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/bismark/summary/meta.yml

@@ -19,7 +19,7 @@ tools:
       homepage: https://github.com/FelixKrueger/Bismark
       documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
       doi: 10.1093/bioinformatics/btr167
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - bam:
       type: file

modules/blast/blastn/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
       documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
       doi: 10.1016/S0022-2836(05)80360-2
-        licence: ['US-Government-Work']
+      licence: ["US-Government-Work"]
 input:
   - meta:
       type: map

modules/blast/makeblastdb/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
       documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
       doi: 10.1016/S0022-2836(05)80360-2
-          licence: ['US-Government-Work']
+      licence: ["US-Government-Work"]
 input:
   - fasta:
       type: file

modules/bowtie/align/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://bowtie-bio.sourceforge.net/index.shtml
       documentation: http://bowtie-bio.sourceforge.net/manual.shtml
       arxiv: arXiv:1303.3997
-          licence: ['Artistic-2.0']
+      licence: ["Artistic-2.0"]
 input:
   - meta:
       type: map

modules/bowtie/build/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://bowtie-bio.sourceforge.net/index.shtml
       documentation: http://bowtie-bio.sourceforge.net/manual.shtml
       arxiv: arXiv:1303.3997
-          licence: ['Artistic-2.0']
+      licence: ["Artistic-2.0"]
 input:
   - fasta:
       type: file

modules/bowtie2/align/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
       documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
       doi: 10.1038/nmeth.1923
-          licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/bowtie2/build/meta.yml

@@ -14,7 +14,7 @@ tools:
       homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
       documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
       doi: 10.1038/nmeth.1923
-          licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - fasta:
       type: file

modules/bwa/aln/meta.yml

@@ -17,7 +17,7 @@ tools:
       homepage: http://bio-bwa.sourceforge.net/
       documentation: http://bio-bwa.sourceforge.net/
       doi: "10.1093/bioinformatics/btp324"
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 
 input:
   - meta:

modules/bwa/index/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: http://bio-bwa.sourceforge.net/
       documentation: http://www.htslib.org/doc/samtools.html
       arxiv: arXiv:1303.3997
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - fasta:
       type: file

modules/bwa/mem/meta.yml

@@ -16,7 +16,7 @@ tools:
       homepage: http://bio-bwa.sourceforge.net/
       documentation: http://www.htslib.org/doc/samtools.html
       arxiv: arXiv:1303.3997
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/bwa/sampe/meta.yml

@@ -18,7 +18,7 @@ tools:
       homepage: http://bio-bwa.sourceforge.net/
       documentation: http://bio-bwa.sourceforge.net/
       doi: "10.1093/bioinformatics/btp324"
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 
 input:
   - meta:

modules/bwa/samse/meta.yml

@@ -19,7 +19,7 @@ tools:
       homepage: http://bio-bwa.sourceforge.net/
       documentation: http://bio-bwa.sourceforge.net/
       doi: "10.1093/bioinformatics/btp324"
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 
 input:
   - meta:

modules/bwamem2/index/meta.yml

@@ -12,7 +12,7 @@ tools:
         a large reference genome, such as the human genome.
       homepage: https://github.com/bwa-mem2/bwa-mem2
       documentation: https://github.com/bwa-mem2/bwa-mem2#usage
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - fasta:
       type: file

modules/bwamem2/mem/meta.yml

@@ -16,7 +16,7 @@ tools:
       homepage: https://github.com/bwa-mem2/bwa-mem2
       documentation: http://www.htslib.org/doc/samtools.html
       arxiv: arXiv:1303.3997
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bwameth/align/meta.yml

@@ -19,7 +19,7 @@ tools:
       homepage: https://github.com/brentp/bwa-meth
       documentation: https://github.com/brentp/bwa-meth
       arxiv: arXiv:1401.1129
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/bwameth/index/meta.yml

@@ -15,7 +15,7 @@ tools:
       homepage: https://github.com/brentp/bwa-meth
       documentation: https://github.com/brentp/bwa-meth
       arxiv: arXiv:1401.1129
-        licence: ['MIT']
+      licence: ["MIT"]
 input:
   - fasta:
       type: file

modules/cat/cat/meta.yml

@@ -10,7 +10,7 @@ tools:
       homepage: None
       documentation: https://man7.org/linux/man-pages/man1/cat.1.html
       tool_dev_url: None
-      licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - files_in:
       type: file

modules/cat/fastq/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: |
         The cat utility reads files sequentially, writing them to the standard output.
       documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
-        licence: ['GPL-3.0-or-later']
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map

modules/checkm/lineagewf/meta.yml

@@ -19,7 +19,7 @@ tools:
       documentation: https://github.com/Ecogenomics/CheckM/wiki
       tool_dev_url: https://github.com/Ecogenomics/CheckM
       doi: "10.1101/gr.186072.114"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/chromap/chromap/meta.yml

@@ -21,7 +21,7 @@ tools:
       documentation: https://github.com/haowenz/chromap
       tool_dev_url: https://github.com/haowenz/chromap
       doi: ""
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

modules/chromap/index/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://github.com/haowenz/chromap
       tool_dev_url: https://github.com/haowenz/chromap
       doi: ""
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - fasta:

modules/clonalframeml/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: https://github.com/xavierdidelot/clonalframeml/wiki
       tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML
       doi: "10.1371/journal.pcbi.1004041"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/cmseq/polymut/meta.yml

@@ -17,7 +17,7 @@ tools:
       homepage: https://github.com/SegataLab/cmseq
       documentation: https://github.com/SegataLab/cmseq
       tool_dev_url: https://github.com/SegataLab/cmseq
-      licence: ['MIT License']
+      licence: ["MIT License"]
 
 input:
   - meta:

modules/cnvkit/batch/meta.yml

@@ -10,7 +10,7 @@ tools:
         CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
       homepage: https://cnvkit.readthedocs.io/en/stable/index.html
       documentation: https://cnvkit.readthedocs.io/en/stable/index.html
-      licence: ['Apache-2.0']
+      licence: ["Apache-2.0"]
 params:
   - outdir:
       type: string

modules/cooler/cload/meta.yml

@@ -9,7 +9,7 @@ tools:
       documentation: https://cooler.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/open2c/cooler
       doi: "10.1093/bioinformatics/btz540"
-      licence: ['BSD-3-clause']
+      licence: ["BSD-3-clause"]
 
 input:
   - meta:

modules/cooler/digest/meta.yml

@@ -10,7 +10,7 @@ tools:
       documentation: https://cooler.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/open2c/cooler
       doi: "10.1093/bioinformatics/btz540"
-      licence: ['BSD-3-Clause']
+      licence: ["BSD-3-Clause"]
 
 input:
   - fasta:

modules/cooler/dump/meta.yml

@@ -9,7 +9,7 @@ tools:
       documentation: https://cooler.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/open2c/cooler
       doi: "10.1093/bioinformatics/btz540"
-      licence: ['BSD-3-Clause']
+      licence: ["BSD-3-Clause"]
 
 input:
   - meta:

modules/cooler/merge/meta.yml

@@ -9,7 +9,7 @@ tools:
       documentation: https://cooler.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/open2c/cooler
       doi: "10.1093/bioinformatics/btz540"
-      licence: ['BSD-3-clause']
+      licence: ["BSD-3-clause"]
 
 input:
   - meta:

modules/cooler/zoomify/meta.yml

@@ -9,7 +9,7 @@ tools:
       documentation: https://cooler.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/open2c/cooler
       doi: "10.1093/bioinformatics/btz540"
-      licence: ['BSD-3-clause']
+      licence: ["BSD-3-clause"]
 
 input:
   - meta:

modules/csvtk/concat/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: http://bioinf.shenwei.me/csvtk
       tool_dev_url: https://github.com/shenwei356/csvtk
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/csvtk/split/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: https://bioinf.shenwei.me/csvtk/
       tool_dev_url: https://github.com/shenwei356/csvtk
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/custom/dumpsoftwareversions/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: Custom module used to dump software versions within the nf-core pipeline template
       homepage: https://github.com/nf-core/tools
       documentation: https://github.com/nf-core/tools
-      licence: ['MIT']
+      licence: ["MIT"]
 input:
   - versions:
       type: file

modules/custom/getchromsizes/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       tool_dev_url: https://github.com/samtools/samtools
       doi: 10.1093/bioinformatics/btp352
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - fasta:
@@ -33,7 +33,6 @@ output:
       description: File containing software version
       pattern: "versions.yml"
 
-
 authors:
   - "@tamara-hodgetts"
   - "@chris-cheshire"

modules/cutadapt/meta.yml

@@ -11,7 +11,7 @@ tools:
         Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
       documentation: https://cutadapt.readthedocs.io/en/stable/index.html
       doi: DOI:10.14806/ej.17.1.200
-      licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/damageprofiler/meta.yml

@@ -18,7 +18,7 @@ tools:
       documentation: https://damageprofiler.readthedocs.io/
       tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler
       doi: "10.1093/bioinformatics/btab190"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/dastool/dastool/meta.yml

@@ -20,7 +20,7 @@ tools:
       documentation: https://github.com/cmks/DAS_Tool
       tool_dev_url: https://github.com/cmks/DAS_Tool
       doi: "10.1038/s41564-018-0171-1"
-      licence: ['BSD']
+      licence: ["BSD"]
 
 input:
   - meta:
@@ -47,7 +47,6 @@ input:
       type: val
       description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond]
 
-
 output:
   - meta:
       type: map

modules/dastool/scaffolds2bin/meta.yml

@@ -20,7 +20,7 @@ tools:
       documentation: https://github.com/cmks/DAS_Tool
       tool_dev_url: https://github.com/cmks/DAS_Tool
       doi: "10.1038/s41564-018-0171-1"
-      licence: ['BSD']
+      licence: ["BSD"]
 
 input:
   - meta:

modules/dedup/meta.yml

@@ -14,7 +14,7 @@ tools:
       documentation: https://dedup.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/apeltzer/DeDup
       doi: "10.1186/s13059-016-0918-z"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:
@@ -54,7 +54,5 @@ output:
       description: Dedup log information
       pattern: "*log"
 
-
-
 authors:
   - "@jfy133"

modules/deeparg/downloaddata/meta.yml

@@ -14,7 +14,7 @@ tools:
       documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
       tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
       doi: "10.1186/s40168-018-0401-z"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - none: There is no input. This module downloads a pre-built database for use with deepARG.

modules/deeparg/predict/meta.yml

@@ -16,7 +16,7 @@ tools:
       documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
       tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
       doi: "10.1186/s40168-018-0401-z"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

modules/deeptools/computematrix/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://deeptools.readthedocs.io/en/develop/index.html
       tool_dev_url: https://github.com/deeptools/deepTools
       doi: "10.1093/nar/gku365"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/deeptools/plotfingerprint/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://deeptools.readthedocs.io/en/develop/index.html
       tool_dev_url: https://github.com/deeptools/deepTools
       doi: "10.1093/nar/gku365"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/deeptools/plotheatmap/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://deeptools.readthedocs.io/en/develop/index.html
       tool_dev_url: https://github.com/deeptools/deepTools
       doi: "10.1093/nar/gku365"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/deeptools/plotprofile/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://deeptools.readthedocs.io/en/develop/index.html
       tool_dev_url: https://github.com/deeptools/deepTools
       doi: "10.1093/nar/gku365"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/deepvariant/meta.yml

@@ -10,7 +10,7 @@ tools:
       documentation: https://github.com/google/deepvariant
       tool_dev_url: https://github.com/google/deepvariant
       doi: "https://doi.org/10.1038/nbt.4235"
-      licence: ['BSD-3-clause']
+      licence: ["BSD-3-clause"]
 
 input:
   - meta:

modules/delly/call/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/dellytools/delly/blob/master/README.md
       tool_dev_url: None
       doi: "DOI:10.1093/bioinformatics/bts378"
-      licence: ['BSD-3-Clause']
+      licence: ["BSD-3-Clause"]
 
 input:
   - meta:

modules/diamond/blastp/meta.yml

@@ -12,7 +12,7 @@ tools:
     documentation: https://github.com/bbuchfink/diamond/wiki
     tool_dev_url: https://github.com/bbuchfink/diamond
     doi: "doi:10.1038/s41592-021-01101-x"
-    licence: ['GPL v3.0']
+    licence: ["GPL v3.0"]
 
 input:
   - meta:

modules/diamond/blastx/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: https://github.com/bbuchfink/diamond/wiki
       tool_dev_url: https://github.com/bbuchfink/diamond
       doi: "doi:10.1038/s41592-021-01101-x"
-      licence: ['GPL v3.0']
+      licence: ["GPL v3.0"]
 
 input:
   - meta: